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  Memory Optimization for the Octopus Scientific Code

Alberdi-Rodriguez, J., Rubio, A., Oliveira, M., Charalampidou, A., & Folias, D. (in preparation). Memory Optimization for the Octopus Scientific Code.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-0024-C453-4 Version Permalink: https://hdl.handle.net/21.11116/0000-0007-38A3-2
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Alberdi-Rodriguez__2015_1022-1.pdf (Preprint), 2MB
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http://nano-bio.ehu.es/memory-optimization-octopus-scientific-code (Preprint)
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https://dx.doi.org/10.5281/zenodo.825543 (Preprint)
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 Creators:
Alberdi-Rodriguez, J.1, 2, Author
Rubio, A.1, 3, 4, Author           
Oliveira, M.5, Author
Charalampidou, A.6, 7, Author
Folias, D.6, 7, Author
Affiliations:
1Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F, ou_persistent22              
2Department of Computer Architecture and Technology, University of the Basque Country UPV/EHU, Donostia, Spain, ou_persistent22              
3Theory Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck Society, ou_2074320              
4Theory, Fritz Haber Institute, Max Planck Society, ou_634547              
5Dep. Physique, Université of Liège, ou_persistent22              
6Greek Research and Technology Network, Athens, Greece , ou_persistent22              
7Scientific Computing Center, Aristotle University of Thessaloniki, Greece, ou_persistent22              

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 Abstract: Octopus is a software package for density-functional theory (DFT), and its time-dependent (TDDFT) variant. Linear Combination of the Atomic Orbitals (LCAO) is performed previous to the actual DFT run. LCAO is used to get an initial guess of densities, and therefore, to start with the Self Consistent Field (SCF) of the Ground-State (GS). System initialization and LCAO steps consume a large amount of memory and do not demonstrate good performance. In this study, extensive profiling has been performed, in order to identify large matrices and scaling behaviour of initialization and LCAO. Alternative implementations of LCAO in Octopus have been investigated in order to optimize memory usage and performance of LCAO approach. Use of ScaLAPACK library led to significant improvement of memory allocation and performance. Benchmark tests have been performed on MareNostrum III HPC system using various combinations of atomic systems’ sizes and numbers of CPU cores.

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Language(s): eng - English
 Dates: 2015
 Publication Status: Not specified
 Pages: 15
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 Table of Contents: -
 Rev. Type: No review
 Identifiers: DOI: 10.5281/zenodo.825543
 Degree: -

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